smriprep

Package Info

KeyValue
Namesmriprep
TitleStructural MRI data preprocessing pipeline
Package version0.9.2
Build3
Base imagenipreps/smriprep:0.9.2
MaintainerMahdieh Dashtbani-Moghari (mahdieh.dashtbanimoghari@sydney.edu.au)
Info URLhttps://www.nipreps.org/smriprep/master/index.html

SMRIPrep: a structural MRI data preprocessing pipeline including Freesurfer

Required licenses

NameURLDescription
freesurferhttps://surfer.nmr.mgh.harvard.edu/registration.htmlsMRIPRep uses FreeSurfer tools, which require a license to run.

Command

KeyValue
Taskarcana.bids:bids_app
Operates onsession

Inputs

NameRequired data-typeDefault column data-typeDescription
T1wmedimage/nifti-gz-xmedimage/dicom-seriesT1-weighted anatomical scan
T2wmedimage/nifti-gz-xmedimage/dicom-seriesT2-weighted anatomical scan

Outputs

NameRequired data-typeDefault column data-typeDescription
smriprepgeneric/directorygeneric/directoryPreprocessed sMRI data

Parameters

NameData typeDescription
smriprep_flagsstrCommand line flags passed on directly to sMRIPrep
json_editsstrJQ filters (https://devdocs.io/jq/) to apply to JSON side-cars in order to handle special cases where the dcm2niix fails to produce valid a BIDS